Project description

This product, eke.biomarker, provides display and RDF ingest of the
biomarkers being studied by the Early Detection Research Network (EDRN).
Biomarkers are chemical indicators for disease, and in the case of EDRN, the
disease being pursued is cancer. This package lets a researcher browse,
search for, and discover interesting biomarkers, determine how research
progress is being made, find out statistical values of the biomarkers, and so
forth. These features are integral to the EDRN Knowledge Environment (EKE).
EDRN uses the EKE to make it easy to discover, share, search for, and retrieve
all of EDRN’s collective knowledge, including cancers and other diseases,
protocols, specimens, participants, staff, and — as in the case of this
product — biomarkers.

Although intended for the EDRN public portal, it can be installed in any
Plone compatible site.

You can skip the ZCML slug if you are going to explicitly include the package
from another package’s configure.zcml file.

Changelog

What follows is a history of changes from release to release. Where issue IDs
are listed below, you can find out more about them by visiting the issue
tracker at https://oodt.jpl.nasa.gov/jira/browse/CA.

1.1.13 — Certified HGNNNNNNNC!

CA-1235 - Make biomarkers link ID end with HGNC name

CA-1238 - Add free text search to Biomarkers

CA-1247 - Link back to BioMuta from EDRN Portal’s biomarkers

CA-1264 - Add Clinical Certification flags

1.1.12 — Let’s Not Talk

CA-1229 - Discussion re-enabled after upgrade

1.1.11 — Bio-TASTIC!

Adds the PIs-by-Biomarkers report plus a menu of (future) reports

CA-1206 - “No resources” appears on a biomarker–body-system when there are
no publications, not if there are no resources

1.1.8 — Lies, Damn Lies, and Statistics

CA-1090 - For biomarkers, show a “-” or “N/A” or SOMETHING for prevalence,
NPV, and PPV if they’re zero or not given.

1.1.7 — Upgrades

Made compatible with Plone 4.1.5.

CA-1010 - Show blank if values are 0 or 0.0

1.1.6 — Test Support

This release includes:

Depending on just Plone the framework instead of Plone the application.

1.1.5 — Dataset Linkages

This release includes:

CA-784: Add ability to associate eCAS datasets with Biomarker records in the
BMDB

(No issue ID): Dataset links should go directly into eCAS

1.1.4 — Resiliency: the bread and butter of PvP

This release makes functional tests more resilient.

1.1.3 — Let’s Collaborate!

This release includes:

A plone.app.testing layer.

Support for edrnsite.collaborations

Re-attaches biomarkers that indicate their collaborative group back to the
“Collaborative Group” (from edrnsite.collaborations) objects to which they
“belong”.

1.1.2 — Upgrade Cleanup

This release updates the GenericSetup profile to 4, provides upgrade steps to
that profile, and makes the testing and development harness depend on “trunk”
level of other eggs instead of on released versions of those eggs.

1.1.1 — Unique IDs

This release replaces the unique ID generation method for “Study Statistics”
objects from the “generateUniqueId” method (acquired from who knows where
(possibly CacheFu?)) to UUIDs, the generation of which is part of the standard
library.

0.0.6 — Open Door Policy

For this release, we’re exposing more information about biomarkers. Instead
of making unapproved biomarkers private and requiring a log in to view them,
you can now view basic information about them. Full details require a login.
For more information, see https://oodt.jpl.nasa.gov/jira/browse/CA-650.

0.0.1 — Security Ingest

0.0.0 — Unreleased

Initial release into beta.

Copyright

Copyright 2009-2010 by the California Institute of Technology. ALL RIGHTS
RESERVED.

The Software is owned by Caltech/JPL and is protected by United States
copyright laws and applicable international treaties and/or conventions. The
United States Government may have prior rights to use some or all of the
Software as determined under applicable contracts and license agreements with
Caltech/JPL.

This software was developed at the Jet Propulsion Laboratory, an operating
division of the California Institute of Technology and is not available for
use by any person, organization, or other entity without prior, specific
written permission.